"Have there been conflicts in your school because of ethnicity?" asked the workshop leader. The 40 or so secondary school students looked uneasily at their teachers. After the 1994 genocide, during which Hutu soldiers and militias killed nearly 1 million Tutsis and moderate Hutus, Rwandans were urged to leave behind their divisive ethnic identities and think of themselves simply as Rwandans.

"Don't be afraid to talk and ask questions, even with your teachers around. We need to talk about ethnicity, even if it makes you uncomfortable, because it is part of our history," says Jean Nepo Ndahimana, an education officer leading a day-long peace-building course for secondary school students at Kigali's genocide memorial. The memorial is a place of remembrance and learning for Rwandans and international visitors, built on the mass graves of 250,000 people killed there. It is a joint venture between the UK-based genocide-prevention NGO, the Aegis Trust, and the Rwandan authorities.

Slowly, a student volunteered that in his school children supported by Farg, a government programme assisting those affected by the genocide, have had their notebooks thrown in the toilets. Genocide orphans are looked down on because they cannot afford school fees or decent clothes, he explained. Another student said that the children of parents who are in prison are called Interahamwe, the name of the Hutu militias who participated in the genocide.

In schools across the country, there are worrying signs that children who were not even born during the genocide are perpetuating the ethnic prejudices of their parents, despite the apparent success of the government's reconciliation policies. "There are no open fights in schools, but a lot of whispering behind one's back, a lot of writing on the walls and anonymous letters," says Ndahimana. He showed me a scrunched piece of paper, which was thrown into a school playground. Translated from Kinyarwanda, it read: "Do not be mistaken, you have survived, the work is not yet finished. We will kill you again!"

More than 60% of Rwanda's population is under the age of 24, so their understanding of the genocide is shaped by their families and communities. "There are resentments and ideologies that children learn from their parents and wider communities, and these feelings pose a threat to long-term stability and the economic and social development of the country," says Dr James Smith, CEO of the Aegis Trust.

The organisation believes that the next five to 10 years offer a unique window to reach this generation. Together with a local organisation, the Institute of Research and Dialogue for Peace, it has designed a course on which those born after the genocide, or who were very young at the time, learn how hatred and prejudice can lead to mass violence. They are taught why peace and reconciliation – however difficult – is vital for the future, both personally and nationally. "Learning from the mistakes of the past: that's what we want our youth to do. We want a youth that promotes a stable and peaceful future," says the Aegis Trust's Robert Bayigamba, Rwanda's former minister for youth.

"Left unresolved, the trauma of any atrocity inflicted on an ethnic group is passed to the next generation, lead[ing] to entrenched ethnic tensions and group conflicts," says Mona Weissmark, associate professor of psychology at Northwestern University Feinberg Medical School in Chicago. "This programme helps young people learn about the dangers of prejudice and builds trust between the children of survivors and perpetrators of the genocide."

During the morning workshop, students revisited their country's history and – using role play, storytelling, problem solving and discussions – learned how to develop empathy and good leadership skills, think critically, and form their own opinions.

In the afternoon, students visited the genocide memorial exhibits, walking through rooms filled with victims' photographs, clothes, and skulls and bones stacked behind glass. Pictures of smiling children were accompanied by notes revealing their names, ages, favourite things – and how they died. Many students cried during the visit and sat in stunned silence in the debriefing room afterwards. "What we have seen was harrowing, but it helps us understand the past and build our future," Ndahimana told them. "We have to ask ourselves what can we do to rebuild our country. We are its future."

"The genocide took place when I was too young. Until today, I didn't know its extent. I had a lot of questions. This gave me some answers. It's not easy to say: 'This happened in our country', but it's important we learn from it," says Jean-Claude Rikorimana, 21.

About 11,000 students have attended the "Learning from the past: building the future" course, but it's still a small proportion of the 2.1 million young people aged 15-24 in Rwanda. To reach a wider audience, the Aegis Trust has created a travelling exhibition called "Peacemaking after genocide".

A detailed analysis of the programme by Minerva Research and Media Services reports "a dramatic positive impact", not only on the attitude and behaviour of participating students but also on the entire school. There was greater empathy with students from other ethnic groups and people in need, material support for poor survivors, and anti-genocide clubs were established.

"This visit changed something in our school," said a student who hadn't attended the workshop. "Some students could have bad attitudes, like hating your colleague. But with the discussions we had after the visit, this has changed."